A new proton therapy facility isunder constructionin Huazhong University of Science and Technology. Scanning magnets play an important role in this device. They can form an arbitrary two-dimensional radiation shape conformal with the tumor. In the pencil beam scanning system, the magnetic fields are excited by time-varying currents and the maximum repetition is up to 50 Hz. Therefore, the temperature rises of two magnets caused by eddy currents should be considered.